Contacts of the strand formed by residues 594 - 600 (chain A) in PDB entry 1JQO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A ILE* 2.7 34.9 - - - +
592A LYS* 2.7 21.1 + - + +
593A GLY* 1.3 72.0 - - - +
595A GLN* 1.3 54.2 + - - +
634A LYS* 3.9 24.2 - - + +
636A THR* 6.2 1.3 - - + -
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Residues in contact with GLN 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A VAL 3.7 13.9 + - - -
563A PRO* 4.7 5.1 - - - +
581A LEU* 4.5 7.0 - - - +
582A PHE* 3.6 33.1 - - + -
587A TYR* 3.1 32.8 + - - -
591A ILE* 3.9 9.0 - - + +
593A GLY 3.4 1.2 + - - +
594A LYS* 1.3 74.0 - - - +
596A GLN* 1.3 99.5 + - - +
597A VAL* 5.1 1.7 - - + +
633A VAL* 4.0 12.1 - - + -
634A LYS 3.2 6.7 + - - +
635A LEU* 2.9 13.0 - - + -
636A THR* 2.8 25.4 + - - +
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Residues in contact with GLN 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A PRO* 4.2 17.5 - - - +
560A PRO* 5.9 3.0 - - - +
562A VAL* 2.9 36.7 - - + +
563A PRO* 3.7 0.2 - - - +
595A GLN* 1.3 104.2 + - - +
597A VAL* 1.3 66.0 + - - +
635A LEU* 4.9 0.4 - - - -
636A THR* 3.1 27.0 + - + +
638A PHE* 3.7 16.2 - - + +
669A ARG* 3.2 36.1 + - - +
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Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A VAL* 3.4 5.6 - - - -
563A PRO* 3.7 15.3 - - + +
565A PHE* 3.3 42.2 - - + -
578A VAL* 5.3 3.4 - - + -
595A GLN* 5.1 2.5 - - + +
596A GLN* 1.3 77.3 - - - +
598A MET* 1.3 64.3 + - - +
624A MET* 3.3 28.0 - - + -
635A LEU* 4.0 19.1 - - + -
636A THR 3.2 2.4 + - - -
637A LEU* 3.4 17.0 - - + +
638A PHE 3.0 20.2 + - - -
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Residues in contact with MET 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TRP* 3.6 24.7 - - + -
533A ILE* 4.1 7.6 - - + -
562A VAL* 3.4 5.9 - - + +
563A PRO 2.9 19.3 + - - +
564A LEU* 3.1 26.4 - - + -
565A PHE* 2.9 29.5 + - - +
597A VAL* 1.3 74.3 - - - +
599A VAL* 1.3 63.5 + - - +
638A PHE* 3.2 68.0 - - + +
640A GLY* 3.9 15.0 - - - -
671A THR* 3.7 12.6 - - + -
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A PHE* 3.4 3.4 - - + +
571A LEU* 3.3 33.0 - - + -
597A VAL 4.2 1.3 - - - +
598A MET* 1.3 79.6 - - - +
600A GLY* 1.3 58.9 + - - +
601A TYR* 3.3 15.0 - - + +
617A LEU* 3.4 22.2 - - + +
620A ALA* 5.3 2.7 - - + -
621A GLN* 4.9 9.4 - - + +
624A MET* 4.2 13.9 - - + -
637A LEU* 3.8 30.3 - - + -
638A PHE 2.8 10.9 + - - +
639A HIS* 5.1 4.9 - - - +
640A GLY 3.0 22.8 + - - -
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Residues in contact with GLY 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A LEU* 4.2 6.1 - - - +
565A PHE 2.8 14.1 + - - -
566A GLU* 2.9 33.9 - - - +
598A MET 4.1 0.6 + - - -
599A VAL* 1.3 73.2 - - - +
601A TYR* 1.3 54.5 + - - -
604A SER* 2.5 24.6 + - - -
617A LEU* 3.5 10.7 - - - +
640A GLY* 4.6 5.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il